Population genetics and forensic DNA for conservation management of the Cypriot mouflon (Ovis orientalis ophion)

The mouflon (Ovis orientalis ophion) is the largest wild terrestrial mammal of Cyprus. Considered as the flagship species of the island, its population (c. 3000 head) has a distribution range limited to the mountainous Paphos Forest and adjacent areas including parts of Troodos National Forest (> 700 Km2). The species is protected by a rigorous national legislation supported since 1996 by management plans carried out by the Game and Fauna Service, and, together with its habitat, by the National Law 152 (I)/2003 for the Protection & Management of Wild Birds and Game Species. The species is listed in the Annexes II and IV of 92/43 Habitats Directive, in the Appendix I of CITES, and classified as “vulnerable” by the IUCN. Poaching, habitat loss, road network building and livestock intrusion (i.e., increased risk of pathogen infection) represent the main threatening factors. We aimed at elucidating the systematic placement of the Cypriot mouflon to enforce its protection within an adaptive conservation framework. Therefore, we attempted to determine its genetic structure and relationships with either historically preserved (Corsica, Sardinia) or recently introduced (central Italy) populations including also GenBank entries from the historical range of the species (Near East). The Game and Fauna Service in collaboration with the Cyprus Veterinary Service collected 63 blood samples: 53 were from mouflons captured in the Paphos forest, eight from captive individuals and two of unknown origin. We also sampled 20 mouflons in Sardinia either in the wild (16) or in captivity (4), and collected scats of both Corsican (19) and central Italy (23: Tuscan Archipelago National Park, 13; Tuscan-Emilian Apennines National Park, 6; Apuan Alps Regional Park, 4) mouflon populations in order to increase geographical scope. We genotyped each sample at the entire mitochondrial DNA Cytochrome-b codifying gene (Cyt-b, 1140 bp) and up to 12 microsatellite DNA markers (Short Tandem Repeats, STR) isolated from goat, sheep and cattle genomes. We found that the Cypriot mouflon strongly diverged from western Mediterranean conspecifics, while North West Iran appeared as the most credited geographic region as the source for its ancient introduction to Cyprus. Although we disclosed much lower mitochondrial and nuclear DNA diversity in the Cypriot than in other island populations, neither evidence of genetic bottleneck nor significant low level of both average pairwise relatedness and inbreeding coefficient was detected. Overall, present mitochondrial and STR dataset worked reliably as crime-fighting tool to tackle illegal mouflon killing in Cyprus. Between 2008 and 2013, the Police and the Game and Fauna Service, in collaboration with the Cyprus Veterinary Services, confiscated 29 samples (meat, hairs, bloodstains) dealing with nine episodes of supposed poaching against the Cypriot mouflon. In all cases, we identified the species in point by sequencing the mtDNA Cyt-b gene. In one case, we were specifically requested to establish if there was a link between three dead mouflons recovered at a roadside and 12 bloodstains collected in the car of suspected poachers at the crime scene. With reference to this case, we were able to match nine bloodstains to two out of the three carcasses (seven with very strong support: Likelihood Ratio >3000 and Random Match Probability <10-3), overall assigning 22 out of 29 samples to the Cypriot mouflon and the remaining ones to wild boar, cow, domestic goat, horse and hare. These results included the first genetic reference for the Cypriot mouflon and the first published material of forensic wildlife investigations in Cyprus

Near infrared reflectance spectroscopy analysis to predict diet composition of a mountain ungulate species

The diet composition of ungulates is important to understand not only their impact on vegetation, but also to understand the consequences of natural and human-driven environmental changes on the foraging behavior of these mammals. In this work, we evaluated the use of near infrared reflectance spectroscopy analysis (NIRS), a quick, economic and non-destructive method, to assess the diet composition of the Pyrenean chamois Rupicapra pyrenaica pyrenaica. Fecal samples (n = 192) were collected from two chamois populations in the French and Spanish Pyrenees. Diet composition was initially assessed by fecal cuticle microhistological analysis (CMA) and categorized into four functional groups, namely: woody, herbaceous, graminoid and Fabaceae plants. Regressions of modified partial least squares and several combinations of scattering correction and derivative treatments were tested. The results showed that models based on the second derivative processing obtained the higher determination coefficient for woody, herbaceous and graminoid plants (RCAL, coefficient of determination in calibration, ranged from 0.86 to 0.91). The Fabaceae group, however, was predicted with lower accuracy (RCAL = 0.71). Even though an agreement between NIRS and CMA methods was confirmed by a Bland-Altman analysis, confidence limits of agreement differed by up to 25%. Our results support the viability of fecal NIRS analysis to study spatial and temporal variations of the Pyrenean chamois' diets in summer and winter when differences in the consumption of woody and annual plants are the greatest. This new use for the NIRS technique would be useful to assess the consequences of global change on the feeding behavior of this mountain ungulate and also in other ungulate counterparts

Variation in the ontogenetic allometry of horn length in bovids along a body mass continuum

International audienceAllometric relationships describe patterns of proportional covariation between morphological, physiological, or life-history traits and the size of the organisms among populations or species (evolutionary allometry), or within population, among individuals measured at similar (static allometry), or different (ontogenetic allometry) age or developmental stages. When expressed on a log-log scale, allometric relationships are often described by a linear regression: log(y) = a + b log(x) where y is the trait size; x the body size; and a and b the allometric intercept and slope, respectively (Huxley, 1932). Because population and species mean trait size and body size used to estimate evolutionary allometry result from the proportional growth of both traits, patterns of evolutionary allometry emerge from variation in ontogenetic allom

Predicting LyC emission of galaxies using their physical and Lyα\alpha emission properties

The primary difficulty in understanding the sources and processes that powered cosmic reionization is that it is not possible to directly probe the ionizing Lyman Continuum (LyC) radiation at that epoch as those photons have been absorbed by the intervening neutral hydrogen in the IGM on their way to us. It is therefore imperative to build a model to accurately predict LyC emission using other properties of galaxies in the reionization era. In recent years, studies have shown that the LyC emission from galaxies may be correlated to their Lya emission. Here, we study this correlation by analyzing thousands of galaxies at high-z in the SPHINX cosmological simulation. We post-process these galaxies with the Lya radiative transfer code RASCAS and analyze the Lya - LyC connection. We find that the Lya and LyC luminosities are strongly correlated with each other, although with dispersion. There is a positive correlation between Lya and LyC escape fractions in the brightest Lya emitters (>$10^{41}$ erg/s), similar to the recent observational studies. However, when we also include fainter Lya emitters (LAEs), the correlation disappears, which suggests that the observed relationship may be driven by selection effects. We also find that bright LAEs are dominant contributors to reionization ($> 10^{40}$ erg/s galaxies contribute $> 90\%$ of LyC emission). Finally, we build predictive models using multivariate linear regression where we use the physical and the Lya properties of simulated galaxies to predict their intrinsic and escaping LyC luminosities with a high degree of accuracy. We find that the most important galaxy properties to predict the escaping LyC luminosity of a galaxy are its escaping Lya luminosity, gas mass, gas metallicity, and SFR. These models can be very useful to predict LyC emissions from galaxies and can help us identify the sources of reionization.Comment: Accepted to Astronomy and Astrophysics (A&A) Journal. 27 pages, 21 Figure

Liouville field theory coupled to a critical Ising model: Non-perturbative analysis, duality and applications

Two different kinds of interactions between a ${Z}_{n}$-parafermionic and a Liouville field theory are considered. For generic values of $n$, the effective central charges describing the UV behavior of both models are calculated in the Neveu-Schwarz sector. For $n=2$ exact vacuum expectation values of primary fields of the Liouville field theory, as well as the first descendent fields are proposed. For $n=1$, known results for Sinh-Gordon and Bullough-Dodd models are recovered whereas for $n=2$, exact results for these two integrable coupled Ising-Liouville models are shown to exchange under a weak-strong coupling duality relation. In particular, exact relations between the parameters in the actions and the mass of the particles are obtained. At specific imaginary values of the coupling and $n=2$, we use previous results to obtain exact information about: (a) Integrable coupled models like Ising-${\cal M}_{p/p'}$, homogeneous sine-Gordon model $SU(3)_2$ or the Ising-XY model; (b) Neveu-Schwarz sector of the $\Phi_{13}$ integrable perturbation of N=1 supersymmetric minimal models. Several non-perturbative checks are done, which support the exact results.Comment: 29 pages, 1 fig., LaTeX file with epsfig, amssymb, 3 references added. To appear in Nucl. Phys.

Prevalence of tick-borne pathogens in ticks collected from the wild mountain ungulates mouflon and chamois in 4 regions of France

Ticks are major vectors of various pathogens of health importance, such as bacteria, viruses and parasites. The problems associated with ticks and vector-borne pathogens are increasing in mountain areas, particularly in connection with global climate change. We collected ticks (n = 2,081) from chamois and mouflon in 4 mountainous areas of France. We identified 6 tick species: Ixodes ricinus, Rhipicephalus bursa, Rh. sanguineus s.l., Haemaphysalis sulcata, H. punctata and Dermacentor marginatus. We observed a strong variation in tick species composition among the study sites, linked in particular to the climate of the sites. We then analysed 791 ticks for DNA of vector-borne pathogens: Babesia/Theileria spp., Borrelia burgdorferi s.l., Anaplasma phagocytophilum, A. marginale, A. ovis, and Rickettsia of the spotted fever group (SFG). Theileria ovis was detected only in Corsica in Rh. bursa. Babesia venatorum (2 sites), Borrelia burgdorferi s.l. (B. afzelii and B. garinii; 2 sites) and Anaplasma phagocytophilum (3 sites) were detected in I. ricinus. Anaplasma ovis was detected at one site in I. ricinus and Rh. sanguineus s.l. SFG Rickettsia were detected at all the study sites: R. monacensis and R. helvetica in I. ricinus at the 3 sites where this tick is present; R. massiliae in Rh. sanguineus s.l. (1 site); and R. hoogstraalii and Candidatus R. barbariae in Rh. bursa in Corsica. These results show that there is a risk of tick-borne diseases for humans and domestic and wild animals frequenting these mountain areas

Seasonal diet composition of Pyrenean chamois is mainly shaped by primary production waves

In alpine habitats, the seasonally marked climatic conditions generate seasonal and spatial differences in forage availability for herbivores. Vegetation availability and quality during the growing season are known to drive life history traits of mountain ungulates. However, little effort has been made to understand the association between plant phenology and changes in the foraging strategies of these mountain dwellers. Furthermore, this link can be affected by the seasonal presence of livestock in the same meadows. The objective of this work was to study the seasonal changes in diet composition of Pyrenean chamois (Rupicapra p. pyrenaica) and its relationship to primary production trends in a Mediterranean alpine environment. Moreover, diet composition in two populations with contrasting livestock pressure was compared in order to study the effect of sheep flocks on the feeding behaviour of chamois. From 2009 to 2012, monthly diet composition was estimated by cuticle microhistological analysis of chamois faeces collected in the eastern Pyrenees. The primary production cycle was assessed by remote sensing, using the Normalized Difference Vegetation Index. Additionally, the diet of sheep sharing seasonally the subalpine and alpine meadows with chamois was analysed. Diet selection of chamois and sheep and their overlap was also assessed. Our results show an intra-annual variation in the diet composition of Pyrenean chamois and demonstrate a strong relationship between plant consumption dynamics and phenology in alpine areas. In addition, Calluna vulgaris, Cytisus spp. and Festuca spp., as well as forbs in the summer, are found to be key forage species for Pyrenean chamois. Furthermore, this study couldn't detect differences between both chamois populations despite the presence of sheep flocks in only one area. However, the detection of a shift in the diet of chamois in both areas after the arrival of high densities of multi-specific livestock suggest a general livestock effect. In conclusion, Pyrenean chamois are well adapted to the variations in the seasonal availability of plants in alpine habitats but could be disturbed by the seasonal presence of livestock. Due to the key plants in their diet, we suggest that population management programmes should focus on the preservation of mixed grasslands composed of patches of shrubs and herbs. The effects of climate change and shrub expansion should be studied as they may potentially affect chamois population dynamics through changes in habitat composition and temporal shifts in forage availability

Molecular DNA identity of the mouflon of Cyprus (Ovis orientalis ophion, Bovidae): Near Eastern origin and divergence from Western Mediterranean conspecific populations

The mouflon population of Cyprus (Ovis orientalis ophion) comprises historically preserved feral descendants of sheep domesticated during the Neolithic. We determined genetic identity of this taxon in order to elucidate its systematic placement and enforce its protection. We used 12 loci of microsatellite DNA to infer genetic relationships between the Cypriot mouflon and either long-time isolated (Corsica, Sardinia) or recently introduced (central Italy) European mouflons (O. o. musimon). We also sequenced the mitochondrial DNA (mtDNA) Cytochrome-b gene to infer the origin of the Cypriot mouflon including many National Centre for Biotechnology Information (NCBI) entries of European and Near Eastern conspecifics. Microsatellites disclosed net divergence between Western Mediterranean and Cypriot mouflon. The latter was included in the highly heterogeneous Near Eastern O. orientalis mtDNA group, Iran representing the most credited region as the source for its ancient introduction to Cyprus. Both international and national legislation protect the mouflon of Cyprus as a wild taxon (O. o. ophion). However, the IUCN Red List of Threatened Species and NCBI include the Cypriot mouflon as subspecies of its respective domestic species, the sheep (O. aries). Unfortunately, people charged with crime against protected mouflon may benefit from such taxonomic inconsistency between legislation and databases, as the latter can frustrate molecular DNA forensic outcomes. Until a definitive light can be shed on Near Eastern O. orientalis systematics, we suggest that the Cypriot mouflon should be unvaryingly referred to as O. o. ophion in order not to impair conservation in the country where it resides